rs984298

chr13-108803822-A-Gchr13-108803822-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001198950.3(MYO16):c.742-2857A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.72 in 152,038 control chromosomes in the GnomAD database, including 40,804 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.72 (40804 hom., cov: 32)
• Consequence: MYO16 NM_001198950.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207

Genes affected

MYO16 (HGNC:29822): (myosin XVI) This gene encodes an unconventional myosin protein. The encoded protein has been proposed to act as a serine/threonine phosphatase-1 targeting or regulatory subunit. Studies in a rat cell line suggest that this protein may regulate cell cycle progression. A variant within this gene may be associated with susceptibility to schizophrenia and elevated expression of this gene has been observed in the frontal cortex of human schizophrenia patients. [provided by RefSeq, Mar 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO16	NM_001198950.3	c.742-2857A>G		intron_variant		ENST00000457511.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO16	ENST00000457511.7	c.742-2857A>G		intron_variant		1	NM_001198950.3	A2
MYO16	ENST00000356711.7	c.676-2857A>G		intron_variant		1		P2
MYO16	ENST00000251041.10	c.676-2857A>G		intron_variant		5
MYO16	ENST00000375857.6	n.62-2857A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.720 AC: 109439 AN: 151920 Hom.: 40770 Cov.: 32

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.884

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.845

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.879

Gnomad FIN AF: 0.833

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.763

Gnomad OTH AF: 0.742

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.720 AC: 109524 AN: 152038 Hom.: 40804 Cov.: 32 AF XY: 0.728 AC XY: 54126 AN XY: 74302

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.801

Gnomad4 ASJ AF: 0.845

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.881

Gnomad4 FIN AF: 0.833

Gnomad4 NFE AF: 0.763

Gnomad4 OTH AF: 0.745

Alfa AF: 0.741 Hom.: 9047

Bravo AF: 0.709

Asia WGS AF: 0.911 AC: 3169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	3.2
Dann	Benign	0.34

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs984298; hg19: chr13-109456170;